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### 5.3 QTLClustInfo

When a QTL clustering has been done using QTLClust See QTLCLust, the result can be formatted using QTLClustInfo. This program allows user to get for a given trait, a given chromosome and a given clustering model, tables in which the results are summarized. QTLClustInfo computes also extra statistics as mahalanobis distances between the QTL of the clustering model, the unconditional confidence intervals (UCI) of these QTL and the predicted values of the observed QTL according to the clustering model.

#### 5.3.1 Command Line Options

Option | Usage | Type | Explanation
--- | --- | --- | ---
`-o,--output` | required | string | The output file
`-c,--chr` | required | string | The name of the chromosome.
`-t,--trait` | required | string | The name of the trait.
`-r,--clust` | required | string | The clustering result file.
`-b,--best` | required | integer | The number of QTL for the best model.
`--kmin` | required | integer | The minimal value to compute the UCI.
`--kmax` | required | integer | The maximal value to compute the UCI.

For example, we focus on the chromosome ``8`' for the trait called ``FT`' for which we have previously performed a QTL clustering via QTLClust. We want to display the result of the clustering for the best model supposed to be the model with 5 QTL. We also want to compute the UCI by averaging over the clustering models from 1 QTL to 10 QTL. Thus we use the command

         %java org.metatqtl.main.QTLClustInfo \
         >     -c 8 -t FT -r clust_res.txt -b 5 --kmin 1 --kmax 10 -o table.txt

The result of this command is dumped into the file `table.txt` which looks like this

         ##
         # Meta-QTL Table
         ##
         --
         QTL     Position        Weight  Distance        CI(95%) UCI(95%)
         --
         1       14.64   0.06    6.21    11.72   11.72
         2       75.39   0.37    1.26    6.25    8.97
         3       89.68   0.42    2.64    3.79    4.24
         4       114.47  0.07    5.2     11.14   11.62
         5       165.25  0.09    -       13.86   13.86
         --
         ##
         # Observed QTL Table
         ##
         --
         QTL   Position   CI(95%)   Predicted   Memberships 1 --> 5
         --
         Pioneer_HT_1    1.91    20.46   14.64   1       0       0       0       0
         Poupard_2001_DPS_10     20.85   14.31   14.64   1       0       0       0       0
         Pioneer_HT_2    62.7    24.62   75.39   0       1       0       0       0
         Lubberstedt_1997_HT_17  74.15   14.31   75.39   0       1       0       0       0
         Bouchez_2002_SD_1       74.86   14.31   75.39   0       1       0       0       0
         Poupard_2001_DPS_11     76.1    16.7    75.53   0       0.99    0.01    0       0
         Moreau_1998_SD_5        67.72   28.62   75.68   0       0.98    0.02    0       0
         Bohn_2000_DPS_11        79.23   14.9    75.96   0       0.96    0.04    0       0
         Vladutu_1999_DPS_2      73.04   26.26   76.1    0       0.95    0.05    0       0
         Rebai_1997_SD_18        59.86   63.15   78.96   0       0.75    0.25    0       0
         Chardon_2005b_SD_1      70.96   73.74   81.64   0       0.58    0.41    0.01    0
         Charcosset_unpub_SD_7   71.13   71.42   81.64   0       0.58    0.41    0.01    0
         Chardon_2005b_DPS_1     70.96   74.75   81.78   0       0.57    0.42    0.01    0
         Groh_1998_HT_6  81.08   32.61   81.96   0       0.54    0.46    0       0
         Mechin_2001_SD_4        82.66   21.44   83.25   0       0.45    0.55    0       0
         Rebai_1997_SD_4 83.22   27.4    83.68   0       0.42    0.58    0       0
         Rebai_1997_SD_31        83.96   30.97   84.11   0       0.39    0.61    0       0
         Blanc_SXflofch8 85.04   37.98   84.39   0       0.37    0.63    0       0
         Chardon_2005b_DPS_2     90.64   75.22   84.49   0       0.37    0.58    0.04    0
         Chardon_2005b_SD_2      90.64   47.75   86.17   0       0.28    0.7     0.02    0
         Groh_1998_SD_5  87.6    29.56   86.82   0       0.2     0.8     0       0
         Blanc_SDflofch8 91.05   25.99   88.97   0       0.05    0.95    0       0
         Moreau_1998_SD_6        93.8    11.92   89.68   0       0       1       0       0
         Vladutu_1999_DPS_1      88.39   10.15   89.68   0       0       1       0       0
         Chardon_2005a_SD_1      91.39   14.31   89.68   0       0       1       0       0
         Chardon_2005a_DPS_1     91.39   7.13    89.68   0       0       1       0       0
         Barierre_2005_SD_3      87.52   9.53    89.68   0       0       1       0       0
         Vladutu_1999_HT_1       88.39   10.15   89.68   0       0       1       0       0
         Blanc_SFflofch8 103.31  31.01   95.64   0       0.01    0.79    0.21    0
         Pioneer_HT_3    112.74  12.31   114.47  0       0       0       1       0
         Ribaut_1996_SD_4        126.15  28.46   114.47  0       0       0       1       0
         Pioneer_HT_4    169.52  19.01   165.25  0       0       0       0       1
         Cardinal_2001_DPS_7     167.11  45.98   165.25  0       0       0       0       1
         Lubberstedt_1997_HT_16  156.52  26.22   165.25  0       0       0       0       1
         --